RNFtools is an associate software package for RNF, a generic format for assigning read names of simulated Next-Generation Sequencing reads. The format aims to remove dependency of evaluation tools of read mappers on the used read simulators.
RNFtools consist of three principal parts:
- MIShmash (MIS => SIM => simulation) - a tool for simulating NGS reads in RNF format using existing simulators.
- LAVEnder (LAVE => EVAL => evaluation) - a tool for evaluation of NGS read mappers using simulated reads in RNF format.
- RNF format library - a Python library for handling the RNF format.
Technically, the entire RNFtools package is based on SnakeMake, a Make-like Python-based software developed for creating bioinformatics pipelines. The resulting pipelines are fully reproducible and they can be distributed as single SnakeMake files.
There exists also a console variant of RNFtools with a basic functionality (see Command-line tool).
1.1. How to start with RNFtools¶
First, we recommend to start with Tutorials which demonstrates how to install RNFtools and how to use it. All examples are also located in a dedicated directory. When you get familiar with basics, the main source of information will be Reference.